EdgeExpressDB (eeDB)

DESCRIPTION: EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets. It is designed for scaling beyond Petabytes and 10^13 objects. For those interested in installing your own instances of EEDB the source code is available via CPAN and is being further developed within the Omics Science Center by Jessica Severin.

MuMRescueLite

DESCRIPTION: MuMRescueLite is the software that enable to use the tag sequencies of mapped to multiple loci to the genome, for the expression analysis. At the mapping of short sequence tags of CAGE or ChIP-Seq to the genome, sequence tags that map to multiple genomic loci (multi-mapping tags or MuMs), are routinely omitted from further analysis, leading to experimental bias and reduced coverage. MuMRescueLite probabilistically reincorporates multi-mapping tags into mapped short read data with acceptable computational requirements.

REQUIREMENTS: Python2.4 or later; platform is same to the Python itself.

Cross-mapping correction software

DESCRIPTION: Modern high-throughput technologies enable deep sequencing of non-coding RNA species, such as miRNAs, on an unprecedented scale. When mapping such small RNAs to the genome, cross-mapping may occur, in which RNA sequences originating from one genomic locus are inadvertently mapped to a different locus. This may give rise to spurious novel RNAs, as well as spurious editing sites in known miRNAs. The cross-mapping correction software is a Python script that aims to correct for such cross-mapping effects.

SAMPLE DATASET: A sample data set is included with the software package.

 Sequence data

All published RIKEN sequence data have been submitted to the public databases.

1. Use of RIKEN sequence data

Note: Please note that RIKEN has assembled some data using some EST data from other sources. Because DDBJ cannot provide RIKEN with accession numbers for data which include data sources outside of RIKEN, some of the total FANTOM3 data cannot be submitted to DDBJ and are not included in the RIKEN data posted at DDBJ.

All sequence data files are compressed in the RIKEN Mouse Encyclopedia sequence data archive and can be downloaded via HTTP. Compressed files can be expanded to their original form using "uncompress". When you download these files please email to us at as we would like to keep track of users.

Note: Depending on the browser you use, you may have some troubles for downloading the files. If you do, please select the "Save link as" function on your browser as this should alleviate any problems.